Sound Agriculture Company, Emeryville, CA, USA.
Sci Rep. 2023 Aug 17;13(1):12915. doi: 10.1038/s41598-023-38356-7.
Epigenetic variation in plant populations is an important factor in determining phenotype and adaptation to the environment. However, while advances have been made in the molecular and computational methods to analyze the methylation status of a given sample of DNA, tools to profile and compare the methylomes of multiple individual plants or groups of plants at high resolution and low cost are lacking. Here, we describe a computational approach and R package (sounDMR) that leverages the benefits of long read nanopore sequencing to enable robust identification of differential methylation from complex experimental designs, as well as assess the variability within treatment groups and identify individual plants of interest. We demonstrate the utility of this approach by profiling a population of Arabidopsis thaliana exposed to a demethylating agent and identify genomic regions of high epigenetic variability between individuals. Given the low cost of nanopore sequencing devices and the ease of sample preparation, these results show that high resolution epigenetic profiling of plant populations can be made more broadly accessible in plant breeding and biotechnology.
植物群体中的表观遗传变异是决定表型和适应环境的重要因素。然而，虽然在分析特定 DNA 样本的甲基化状态的分子和计算方法方面已经取得了进展，但缺乏用于高分辨率和低成本地分析多个个体植物或植物群体的甲基组图谱并进行比较的工具。在这里，我们描述了一种计算方法和 R 包（sounDMR），该方法利用长读长纳米孔测序的优势，能够从复杂的实验设计中稳健地识别差异甲基化，并评估处理组内的变异性和鉴定感兴趣的个体植物。我们通过对暴露于去甲基化剂的拟南芥群体进行分析，展示了这种方法的实用性，并鉴定了个体之间高表观遗传变异性的基因组区域。鉴于纳米孔测序设备的低成本和样品制备的简便性，这些结果表明，可以更广泛地在植物育种和生物技术中实现植物群体的高分辨率表观遗传分析。
